Abstract: The present study was designed to evaluate the in vivo nutritional quality of the modified proteins of milk and wheat by cross-linking with microbial transglutaminase (TGase). White Wistar rats were divided into six groups receiving diets that contained casein, cross-linked milk protein, milk protein, cross-linked wheat protein, wheat protein, or a protein free diet. Results showed that cross-linked milk and wheat proteins can support growth, with the animals showing a positive nitrogen balance. Protein true digestibility was similar between casein and non-cross-linked milk protein diets. It was also observed that milk and wheat proteins were not affected by cross-linking concerning several quality parameters: protein efficiency ratio, food efficiency ratio, food transformation index, apparent nitrogen digestibility, true digestibility, biological value, net protein utilization, net protein ratio and protein retention efficiency. Based on these results, it can be suggested that the use of microbial TGase does not affect the nutritional quality of milk or wheat proteins, while improving their physicochemical properties.